Geneva Study Bible
(1) There are none sometimes more unlearned than the learned, but the learned as well as the unlearned must desire wisdom from Christ only.
(a) A man of great estimation and a ruler amongst the Jews.
(b) We know that you are sent from God to teach us.
(c) But he in whom some part of the excellency of God appears. And if Nicodemus had rightly known Christ, he would not only have said that God was with him, but in him, as Paul does in (2 Corinthians 1:19).
(2) The beginning of Christianity consists in this, that we know ourselves not only to be corrupt in part, but to be wholly dead in sin: so that our nature has need to be created anew, with regard to its qualities, which can be done by no other power, but by the divine and heavenly, by which we were first created.
(d) That is, "go in", or "enter", as he expounds himself below in (John 3:5).
(e) The Church: for Christ shows here how we come to be citizens and to have anything to do in the city of God.
(f) How can I who am old be born again? For Nicodemus answers as if Christ's words were only addressed to himself.
(g) That is, fleshly, namely, wholly unclean and under the wrath of God: and therefore this word "flesh" signifies the corrupt nature of man: contrary to which is the Spirit, that is, the man ingrafted into Christ through the grace of the Holy Spirit, whose nature is everlasting and immortal, though the strife of the flesh remains.
(h) With free and wandering blasts as it wishes.
(3) The secret mystery of our regeneration which cannot be comprehended by man's capacity, is perceived by faith, and that in Christ only, because he is both God on earth, and man in heaven, that is to say, man in such a way that he is God also, and therefore almighty: and God in such a way that he is man also, and therefore his power is made manifest to us.
(i) You handle doubtful things even though you have no solid basis for believing them, and yet men believe you: but I teach those things that are of a truth and well known, and you do not believe me.
(k) Only Christ can teach us heavenly things, for no man ascends, etc.
(l) That is, has any spiritual light and understanding, or ever had any, but only the Son of God who came down to us.
(m) Whereas he is said to have come down from heaven, this must be understood as referring to his Godhead, and of the manner of his conception: for Christ's birth upon the earth was heavenly and not earthly, for he was conceived by the Holy Spirit.
(n) That which is proper to the divinity of Christ, is here spoken of the whole Christ, to show us that he is but one person in which two natures are united.
(5) Nothing else but the free love of the Father is the beginning of our salvation, and Christ is he in whom our righteousness and salvation dwells: and faith is the instrument or means by which we apprehend it, and everlasting life is that which is set before us to apprehend.
(o) It is not the same to believe in a thing, and to believe about a thing, for we may not believe in anything except in God alone, but we may believe about anything whatever, says Nazianzene in his Oration of the Spirit.
(6) Christ does not condemn, but rather despising Christ condemns.
(p) That is, to be the cause of the condemning of the world, for indeed sins are the cause of death; however, Christ will still judge the living and the dead.
(q) Not only the people of the Jews, but whoever will believe in him.
(7) The only reason why men refuse the light that is offered to them is wickedness.
(r) That is, the cause of condemnation, which remains in men, unless through God's great benefit they are delivered from it.
(s) That is, he that leads an honest life, and is void of all cunning and deceit.
(t) That is, with God, God as it were going before.
(8) Satan inflames the disciples of John with a fond emulation of their master in order to hinder the course of the gospel: but John, being mindful of his office, not only puts a stop to their endeavours, but also takes occasion by that means to give testimony of Christ, that in him alone the Father has set forth everlasting life.
(u) Why are you trying to better my state? This is every man's lot and portion, that he cannot better himself in the slightest way.
(x) Is nothing else but man, a piece of work made of the slime of the earth.
(y) Is characterized by nothing but corruption, ignorance, dulness, etc.
(z) What he knows fully and perfectly.
(a) That is, very few.
(b) Committed them to his power and will.
(c) Shall not enjoy.
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Beza, Theodore. "Commentary on John 3". "The 1599 Geneva Study Bible". https://beta.studylight.org/
the Week of Proper 20 / Ordinary 25